3-25764224-T-G
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 2P and 15B. PM2BP4_ModerateBP6_Very_StrongBP7BS1
The NM_018297.4(NGLY1):āc.334A>Cā(p.Arg112=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000626 in 1,614,192 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. R112R) has been classified as Likely benign.
Frequency
Consequence
NM_018297.4 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NGLY1 | NM_018297.4 | c.334A>C | p.Arg112= | synonymous_variant | 3/12 | ENST00000280700.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NGLY1 | ENST00000280700.10 | c.334A>C | p.Arg112= | synonymous_variant | 3/12 | 1 | NM_018297.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000427 AC: 65AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000111 AC: 28AN: 251324Hom.: 0 AF XY: 0.0000810 AC XY: 11AN XY: 135814
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1461886Hom.: 0 Cov.: 31 AF XY: 0.0000179 AC XY: 13AN XY: 727244
GnomAD4 genome AF: 0.000440 AC: 67AN: 152306Hom.: 0 Cov.: 32 AF XY: 0.000416 AC XY: 31AN XY: 74476
ClinVar
Submissions by phenotype
Congenital disorder of deglycosylation Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
NGLY1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 23, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at